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Fixing issues found during GPU runtime testing

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This commit is contained in:
Stan Moore
2016-12-20 17:03:46 -07:00
parent 07bee39002
commit 35803c75c9
3 changed files with 65 additions and 29 deletions
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79
src/KOKKOS/fix_eos_table_rx_kokkos.cpp
View File

@ -49,6 +49,13 @@ FixEOStableRXKokkos<DeviceType>::FixEOStableRXKokkos(LAMMPS *lmp, int narg, char
k_error_flag = DAT::tdual_int_scalar("fix:error_flag");
k_warning_flag = DAT::tdual_int_scalar("fix:warning_flag");
k_dHf = DAT::tdual_float_1d("fix:dHf",nspecies);
for (int n = 0; n < nspecies; n++)
k_dHf.h_view(n) = dHf[n];
k_dHf.modify<LMPHostType>();
k_dHf.sync<DeviceType>();
d_dHf = k_dHf.view<DeviceType>();
}
/* ---------------------------------------------------------------------- */
@ -73,6 +80,7 @@ void FixEOStableRXKokkos<DeviceType>::setup(int vflag)
copymode = 1;
int nlocal = atom->nlocal;
double boltz = force->boltz;
mask = atomKK->k_mask.view<DeviceType>();
uCond = atomKK->k_uCond.view<DeviceType>();
uMech = atomKK->k_uMech.view<DeviceType>();
@ -82,16 +90,20 @@ void FixEOStableRXKokkos<DeviceType>::setup(int vflag)
uCGnew = atomKK->k_uCGnew.view<DeviceType>();
dvector = atomKK->k_dvector.view<DeviceType>();
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | UCG_MASK | UCGNEW_MASK | DVECTOR_MASK);
atomKK->modified(execution_space,UCHEM_MASK | DPDTHETA_MASK | UCG_MASK | UCGNEW_MASK);
if (!this->restart_reset)
if (!this->restart_reset) {
atomKK->sync(execution_space,MASK_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXSetup>(0,nlocal),*this);
atomKK->modified(execution_space,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
}
// Communicate the updated momenta and velocities to all nodes
atomKK->sync(Host,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
comm->forward_comm_fix(this);
atomKK->modified(Host,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | DVECTOR_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXTemperatureLookup>(0,nlocal),*this);
atomKK->modified(execution_space,DPDTHETA_MASK);
error_check();
@ -127,6 +139,7 @@ void FixEOStableRXKokkos<DeviceType>::init()
copymode = 1;
int nlocal = atom->nlocal;
double boltz = force->boltz;
mask = atomKK->k_mask.view<DeviceType>();
uCond = atomKK->k_uCond.view<DeviceType>();
uMech = atomKK->k_uMech.view<DeviceType>();
@ -134,13 +147,15 @@ void FixEOStableRXKokkos<DeviceType>::init()
dpdTheta= atomKK->k_dpdTheta.view<DeviceType>();
dvector = atomKK->k_dvector.view<DeviceType>();
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | UCG_MASK | UCGNEW_MASK | DVECTOR_MASK);
atomKK->modified(execution_space,UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK);
if (this->restart_reset)
if (this->restart_reset) {
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | DVECTOR_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXTemperatureLookup>(0,nlocal),*this);
else
atomKK->modified(execution_space,DPDTHETA_MASK);
} else {
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | DVECTOR_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXInit>(0,nlocal),*this);
atomKK->modified(execution_space,UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK);
}
error_check();
@ -172,6 +187,7 @@ void FixEOStableRXKokkos<DeviceType>::post_integrate()
copymode = 1;
int nlocal = atom->nlocal;
double boltz = force->boltz;
mask = atomKK->k_mask.view<DeviceType>();
uCond = atomKK->k_uCond.view<DeviceType>();
uMech = atomKK->k_uMech.view<DeviceType>();
@ -210,6 +226,7 @@ void FixEOStableRXKokkos<DeviceType>::end_of_step()
copymode = 1;
int nlocal = atom->nlocal;
double boltz = force->boltz;
mask = atomKK->k_mask.view<DeviceType>();
uCond = atomKK->k_uCond.view<DeviceType>();
uMech = atomKK->k_uMech.view<DeviceType>();
@ -219,18 +236,24 @@ void FixEOStableRXKokkos<DeviceType>::end_of_step()
uCGnew = atomKK->k_uCGnew.view<DeviceType>();
dvector = atomKK->k_dvector.view<DeviceType>();
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | UCG_MASK | UCGNEW_MASK | DVECTOR_MASK);
atomKK->modified(execution_space,UCHEM_MASK | DPDTHETA_MASK | UCG_MASK | UCGNEW_MASK);
// Communicate the ghost uCGnew
atomKK->sync(Host,UCG_MASK | UCGNEW_MASK);
comm->reverse_comm_fix(this);
atomKK->modified(Host,UCG_MASK | UCGNEW_MASK);
atomKK->sync(execution_space,MASK_MASK | UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXSetup>(0,nlocal),*this);
atomKK->modified(execution_space,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
// Communicate the updated momenta and velocities to all nodes
atomKK->sync(Host,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
comm->forward_comm_fix(this);
atomKK->modified(Host,UCHEM_MASK | UCG_MASK | UCGNEW_MASK);
atomKK->sync(execution_space,MASK_MASK | UCOND_MASK | UMECH_MASK | UCHEM_MASK | DPDTHETA_MASK | DVECTOR_MASK);
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagFixEOStableRXTemperatureLookup2>(0,nlocal),*this);
atomKK->modified(execution_space,DPDTHETA_MASK);
error_check();
@ -265,13 +288,13 @@ void FixEOStableRXKokkos<DeviceType>::energy_lookup(int id, double thetai, doubl
//uTmp = tb->e[itable] + fraction*tb->de[itable];
uTmp = d_table_const.e(ispecies,itable) + fraction*d_table_const.de(ispecies,itable);
uTmp += dHf[ispecies];
uTmp += d_dHf[ispecies];
// mol fraction form:
ui += dvector(ispecies,id)*uTmp;
nTotal += dvector(ispecies,id);
}
}
ui = ui - double(nTotal+1.5)*force->boltz*thetai; // need class variable
ui = ui - double(nTotal+1.5)*boltz*thetai;
}
/* ----------------------------------------------------------------------
@ -344,13 +367,16 @@ template<class DeviceType>
int FixEOStableRXKokkos<DeviceType>::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int ii,jj,m;
HAT::t_efloat_1d h_uChem = atomKK->k_uChem.h_view;
HAT::t_efloat_1d h_uCG = atomKK->k_uCG.h_view;
HAT::t_efloat_1d h_uCGnew = atomKK->k_uCGnew.h_view;
m = 0;
for (ii = 0; ii < n; ii++) {
jj = list[ii];
buf[m++] = uChem[jj];
buf[m++] = uCG[jj];
buf[m++] = uCGnew[jj];
buf[m++] = h_uChem[jj];
buf[m++] = h_uCG[jj];
buf[m++] = h_uCGnew[jj];
}
return m;
}
@ -361,13 +387,16 @@ template<class DeviceType>
void FixEOStableRXKokkos<DeviceType>::unpack_forward_comm(int n, int first, double *buf)
{
int ii,m,last;
HAT::t_efloat_1d h_uChem = atomKK->k_uChem.h_view;
HAT::t_efloat_1d h_uCG = atomKK->k_uCG.h_view;
HAT::t_efloat_1d h_uCGnew = atomKK->k_uCGnew.h_view;
m = 0;
last = first + n ;
for (ii = first; ii < last; ii++){
uChem[ii] = buf[m++];
uCG[ii] = buf[m++];
uCGnew[ii] = buf[m++];
h_uChem[ii] = buf[m++];
h_uCG[ii] = buf[m++];
h_uCGnew[ii] = buf[m++];
}
}
@ -377,12 +406,14 @@ template<class DeviceType>
int FixEOStableRXKokkos<DeviceType>::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
HAT::t_efloat_1d h_uCG = atomKK->k_uCG.h_view;
HAT::t_efloat_1d h_uCGnew = atomKK->k_uCGnew.h_view;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = uCG[i];
buf[m++] = uCGnew[i];
buf[m++] = h_uCG[i];
buf[m++] = h_uCGnew[i];
}
return m;
}
@ -393,13 +424,15 @@ template<class DeviceType>
void FixEOStableRXKokkos<DeviceType>::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
HAT::t_efloat_1d h_uCG = atomKK->k_uCG.h_view;
HAT::t_efloat_1d h_uCGnew = atomKK->k_uCGnew.h_view;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
uCG[j] += buf[m++];
uCGnew[j] += buf[m++];
h_uCG[j] += buf[m++];
h_uCGnew[j] += buf[m++];
}
}

6
src/KOKKOS/fix_eos_table_rx_kokkos.h
View File

@ -105,12 +105,15 @@ class FixEOStableRXKokkos : public FixEOStableRX {
int **tabindex;
double boltz;
void allocate();
void error_check();
int update_table;
void create_kokkos_tables();
//double *dHf;
DAT::tdual_float_1d k_dHf;
typename AT::t_float_1d d_dHf;
typename AT::t_int_1d mask;
typename AT::t_efloat_1d uCond,uMech,uChem,uCG,uCGnew,rho,dpdTheta,duChem;
@ -124,7 +127,6 @@ class FixEOStableRXKokkos : public FixEOStableRX {
int pack_forward_comm(int , int *, double *, int, int *);
void unpack_forward_comm(int , int , double *);
//int *eosSpecies;
};
}

9
src/KOKKOS/pair_exp6_rx_kokkos.cpp
View File

@ -645,7 +645,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
int params_per_line = 5;
char **words = new char*[params_per_line+1];
memory->sfree(params);
memory->destroy_kokkos(k_params,params);
params = NULL;
nparams = maxparam = 0;
@ -723,6 +723,7 @@ void PairExp6rxKokkos<DeviceType>::read_file(char *file)
// load up parameter settings and error check their values
if (nparams == maxparam) {
k_params.template modify<LMPHostType>();
maxparam += DELTA;
memory->grow_kokkos(k_params,params,maxparam,
"pair:params");
@ -823,7 +824,7 @@ void PairExp6rxKokkos<DeviceType>::getParamsEXP6(int id,double &epsilon1,double
nTotal += dvector(ispecies,id);
nTotal_old += dvector(ispecies+nspecies,id);
iparam = mol2param[ispecies];
iparam = d_mol2param[ispecies];
if (iparam < 0 || d_params[iparam].potentialType != exp6PotentialType ) continue;
if (isOneFluidApprox(isite1) || isOneFluidApprox(isite2)) {
@ -840,7 +841,7 @@ void PairExp6rxKokkos<DeviceType>::getParamsEXP6(int id,double &epsilon1,double
fractionOFA = nTotalOFA / nTotal;
for (int ispecies = 0; ispecies < nspecies; ispecies++) {
iparam = mol2param[ispecies];
iparam = d_mol2param[ispecies];
if (iparam < 0 || d_params[iparam].potentialType != exp6PotentialType ) continue;
// If Site1 matches a pure species, then grab the parameters
@ -881,7 +882,7 @@ void PairExp6rxKokkos<DeviceType>::getParamsEXP6(int id,double &epsilon1,double
xMolei_old = dvector(ispecies+nspecies,id)/nTotalOFA_old;
for (int jspecies = 0; jspecies < nspecies; jspecies++) {
jparam = mol2param[jspecies];
jparam = d_mol2param[jspecies];
if (jparam < 0 || d_params[jparam].potentialType != exp6PotentialType ) continue;
if (isite1 == d_params[jparam].ispecies || isite2 == d_params[jparam].ispecies) continue;
rmj = d_params[jparam].rm;